Update 3.32pm: The Housing Minister has said the recent crisis may have brought Fianna Fáil and Fine Gael closer together.

Eoghan Murphy dismissed concerns that the confidence and supply arrangement is in tatters.

The wide consensus in Leinster House is that there will be an election in the first half of next year.

Housing Minister Eoghan Murphy said the arrangement can still survive.

"I don't think it is damaged. I think, obviously, there's always going to be a tension between Fianna Fáil and Fine Gael insofar as us as party members in the Dáil. That will always maintain," he said.

"My impression from what happened over the weekend with the work that the Taoiseach did with Micheál Martin to try and avert an election is that it actually helped strengthen the confidence and supply between the two leaders," he said.

However, a Fianna Fáil TD has said an early election is "inevitable".

John McGuinness said that damage has been done to the country by the crisis over the last few days.

Fine Gael and Fianna Fáil TDs have sought to mend the gap between the parties after the government almost collapsed yesterday.

But John McGuinness says there is only one outcome from this for the confidence and supply arrangement.

"It has been damaged in terms of trust between the two main parties. It has shown a dysfunctional side of Government within the Department of Justice that needs to be repaired quickly," he said.

"I think that damage has been done to this country and I think that an earlier election than what was planned is absolutely inevitable," he added.

Update 9.13am: The agreement between Fine Gael and Fianna Fáil was 'stretched to breaking point' by the whistleblower crisis, according to a Junior Minister.

But Micheal D'Arcy says the agreement isn't broken, and he's not sure an election is inevitable in the Spring.

The government was on the brink of collapsing yesterday before Frances Fitzgerald's resignation as Tánaiste avoided a Christmas election.

Mr D'Arcy admits the confidence and supply arrangement keeping the government up has been sorely tested but isn't convinced an election is inevitable.

"There's really major issues coming up, everybody knows and understands what those issues are, and we as public representatives, members of the Oireachtas, have to get on and deal with them.

"I think it was stretched to breaking point, it isn't broken it's still in place, and over time we'll know if that hypothesis is correct or not."

Michael D'arcy (left) with Paul Keogh.

Update 8.30: Taoiseach Leo Varadkar may use the resignation of Frances Fitzgerald as Tánaiste as an opportunity for a wider reshuffle at Cabinet to embolden the party ahead of any general election, writes Juno McEnroe

Foreign Affairs Minister Simon Coveney is being widely tipped as the next Tánaiste but a decision on the appointment and other potential Cabinet changes are not expected for several days.

A Government spokesman has said that Mr Varadkar could “potentially” make wider changes to the Cabinet make-up.

Several Fine Gael TDs and ministers have said that Mr Coveney would be well placed to step into the role.

“He is loyal, a good debater, and it might help heal any divide after the recent leadership contest between them,” said a Fine Gael source.

Some sources have also mentioned the name of Education Minister Richard Bruton, Social Welfare Minister Regina Doherty, and Arts Minister Heather Humphreys as potential considerations for Tánaiste.

Other sources have noted that Mr Varadkar may be closer to Finance Minister Paschal Donohoe and choose him.

Ms Fitzgerald was defiant as she passed through the selection convention in Dublin Mid-West, having earlier in the day resigned from the Cabinet in order to prevent an “unnecessary” general election.

“I have to say, it has been very tough being at the centre of this political storm, not something I’m used to, not something too many people are used to,” she said.

“It’s also been very hard to get facts on the table and I want to say that to you amid the very frenzied political media atmosphere.”

But she vowed to “vindicate my good name” when she appears before the Disclosures Tribunal after Christmas.

It is expected that Foreign Affairs Minister Simon Coveney will replace her as Tánaiste in the coming days.

Mr Varadkar is facing a major internal backlash from within Fine Gael over his handling of the email scandal, while Mr Flanagan was forced to make a number of abject apologies in the Dáil over his failures and those of his department.

His decision to support Ms Fitzgerald throughout the weekend when he knew more information was to come has come under sharp criticism.

The drama of the day was compounded by the immediate retirement of Noel Waters, secretary general of the Department of Justice, who hit back at criticisms of the department made in the Dáil by Mr Varadkar.

Mr Waters informed staff in the department of his imminent departure after Mr Varadkar lashed out at the “dysfunctional” department.

Mr Varadkar has also launched an external review of why some records were not sent to the tribunal which is due to conclude by Christmas.

Mr Waters later told staff he is retiring with immediate effect, two weeks after he told Mr Flanagan he would retire in February during a phone call in which he revealed the May 15, 2015, McCabe email.

Mr Waters will retire on an annual pension of €100,000, based on actuarial calculations.

In his retirement email, Mr Waters hit out at a “barrage of unwarranted criticism” in the Dáil but said he was leaving “of my own volition”.

The Government press secretary last night said there was no interaction between Mr Waters and Government before his sudden retirement, saying: “Mr Waters has said he took this decision entirely of his own volition.”

He insisted no officials contacted Mr Waters before he retired with immediate effect.

On hearing Ms Fitzgerald’s decision to resign at a “sombre” Cabinet meeting, while colleagues expressed sorrow at events, not one expressed the belief that she should have remained on.

Speaking to the Irish Examiner, Mr Coveney said: “This was a day which was frustrating for Fine Gael and the Government. There was a total change in the national mood because of the way the new emails were presented on Monday and that made it impossible for Fianna Fáil to accept anything less than her resignation.

“And so she had to resign to avoid an election, there was no avoiding that. There are legitimate questions that Frances has to answer and there is a need for political accountability so I don’t criticise Fianna Fail for that.”

In the Dáil, Mr Flanagan was subjected to harsh criticism after he admitted to “failing to realise the significance” of the emails which are at the heart of the controversy.

Asked how he failed to “connect” the fact his secretary general, Noel Waters, retired in the same phone call as he told him of the email, Mr Flanagan said he only realised the seriousness “in hindsight” and that the retirement is “coincidental”.

Key records at the heart of the Maurice McCabe email scandal were for unknown reasons left out of an extensive trawl of thousands of Department records which were subsequently sent to the Charleton tribunal.

Asked to explain why the email was not found by an initial Department of Justice trawl, Mr Flanagan said “my understanding is they are new documents and were not in the previous process”.

Mr Flanagan also apologised in the Dáil for failings at the Department of Justice.

“This is completely unacceptable and I wish to formally apologise to the Taoiseach, to you Ceann Comhairle and to the House,” said Mr Flanagan.

Finance Minister Paschal Donohoe arrived out at Ms Fitzgerald’s convention and gave a 10-minute speech in support of his colleague.

“Rarely has a person of such quality been tested like she has in recent days,” he said.